Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The...

Area of Science:

• Genomics
• Molecular Biology
• Bacterial Chromosome Structure

Background:

• The Escherichia coli chromosome contains unique GC-rich genomic structural elements.
• These elements trigger the formation of post-replication gaps after the replisome passes.

Approach:

• Identified two nearly perfect 222 bp repeats, termed Replication Risk Sequences (RRS), located 650 kb from the dif terminus sequence and flanking the Ter macrodomain.
• Investigated the conservation, essentiality, and functional impact of RRS elements on genome structure and topology.
• Analyzed the role of G-quadruplex structures within RRS in impeding DNA polymerase extension and causing lagging strand single-stranded DNA gaps.

Key Points:

• RRS sequences and their positioning are highly conserved in enterobacteria.
• At least one RRS is essential for cell viability unless a specific genomic region is amplified.
• RRS contain a G-quadruplex on the lagging strand, which hinders DNA polymerase extension, leading to gaps up to 2000 bp long.
• Deletion of both RRS elements significantly impacts global genome structure and topology.

Conclusions:

• RRS elements are hypothesized to function as topological relief valves during chromosome replication and segregation.
• The discovery of RRS fills a gap in understanding genomic sequences that induce transient gap formation.
• Functional analogs of RRS may be widespread, potentially including eukaryotic G-quadruplexes.